3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTGTGTGTGTGTG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_004130.4(GYG1):​c.481+172_481+179dupGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 606,362 control chromosomes in the GnomAD database, including 105 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.028 ( 73 hom., cov: 0)
Exomes 𝑓: 0.019 ( 32 hom. )

Consequence

GYG1
NM_004130.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.285
Variant links:
Genes affected
GYG1 (HGNC:4699): (glycogenin 1) This gene encodes a member of the glycogenin family. Glycogenin is a glycosyltransferase that catalyzes the formation of a short glucose polymer from uridine diphosphate glucose in an autoglucosylation reaction. This reaction is followed by elongation and branching of the polymer, catalyzed by glycogen synthase and branching enzyme, to form glycogen. This gene is expressed in muscle and other tissues. Mutations in this gene result in glycogen storage disease XV. This gene has pseudogenes on chromosomes 1, 8 and 13 respectively. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 3-148997054-T-TTGTGTGTG is Benign according to our data. Variant chr3-148997054-T-TTGTGTGTG is described in ClinVar as [Likely_benign]. Clinvar id is 1196791.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0276 (4137/149796) while in subpopulation AFR AF= 0.0408 (1656/40614). AF 95% confidence interval is 0.0391. There are 73 homozygotes in gnomad4. There are 2071 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 73 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GYG1NM_004130.4 linkuse as main transcriptc.481+172_481+179dupGTGTGTGT intron_variant ENST00000345003.9 NP_004121.2 P46976-1
GYG1NM_001184720.2 linkuse as main transcriptc.481+172_481+179dupGTGTGTGT intron_variant NP_001171649.1 P46976-2
GYG1NM_001184721.2 linkuse as main transcriptc.481+172_481+179dupGTGTGTGT intron_variant NP_001171650.1 P46976-3
GYG1XM_017006275.2 linkuse as main transcriptc.304+172_304+179dupGTGTGTGT intron_variant XP_016861764.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GYG1ENST00000345003.9 linkuse as main transcriptc.481+150_481+151insTGTGTGTG intron_variant 1 NM_004130.4 ENSP00000340736.4 P46976-1

Frequencies

GnomAD3 genomes
AF:
0.0276
AC:
4130
AN:
149680
Hom.:
72
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0407
Gnomad AMI
AF:
0.0299
Gnomad AMR
AF:
0.0197
Gnomad ASJ
AF:
0.0211
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0373
Gnomad FIN
AF:
0.0227
Gnomad MID
AF:
0.0127
Gnomad NFE
AF:
0.0241
Gnomad OTH
AF:
0.0250
GnomAD4 exome
AF:
0.0194
AC:
8861
AN:
456566
Hom.:
32
AF XY:
0.0199
AC XY:
4843
AN XY:
243632
show subpopulations
Gnomad4 AFR exome
AF:
0.0343
Gnomad4 AMR exome
AF:
0.0134
Gnomad4 ASJ exome
AF:
0.0117
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0300
Gnomad4 FIN exome
AF:
0.0217
Gnomad4 NFE exome
AF:
0.0195
Gnomad4 OTH exome
AF:
0.0196
GnomAD4 genome
AF:
0.0276
AC:
4137
AN:
149796
Hom.:
73
Cov.:
0
AF XY:
0.0283
AC XY:
2071
AN XY:
73086
show subpopulations
Gnomad4 AFR
AF:
0.0408
Gnomad4 AMR
AF:
0.0196
Gnomad4 ASJ
AF:
0.0211
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0369
Gnomad4 FIN
AF:
0.0227
Gnomad4 NFE
AF:
0.0241
Gnomad4 OTH
AF:
0.0247

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxApr 13, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10571382; hg19: chr3-148714841; API